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(-) Description

Title :  CRYSTAL STRUCTURE OF AGRA LYTTR DOMAIN IN COMPLEX WITH PROMOTERS
 
Authors :  B. Gopal, K. Rajasree
Date :  19 Jan 15  (Deposition) - 06 Apr 16  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  G,H,I  (1x)
Biol. Unit 4:  J,K,L  (1x)
Keywords :  Dna-Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Gopal, K. Rajasree
Conformational Features Of The Staphylococcus Aureus Agra-Promoter Interactions Rationalize Quorum-Sensing Triggered Gene Expression
Biochem Biophys Rep V. 6 124 2016
PubMed: search  |  Reference-DOI: 10.1016/J.BBREP.2016.03.012

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*CP*AP*GP*TP*TP*AP*AP*GP*AP*AP*T)-3')
    Chains: B, E, H, K
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(P*AP*AP*TP*TP*CP*TP*TP*AP*AP*CP*TP*GP*T)-3')
    Chains: C, F, I, L
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - ACCESSORY GENE REGULATOR A
    Chains: A, D, G, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 140-238
    Gene: AGRA, SACOL2026
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN COL)
    Organism Taxid: 93062
    Strain: COL

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABC         
Biological Unit 2 (1x):    DEF      
Biological Unit 3 (1x):       GHI   
Biological Unit 4 (1x):          JKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC C:10 , GLU J:141binding site for residue EDO C 101
2AC2SOFTWAREDT I:11 , HOH I:203binding site for residue EDO I 102
3AC3SOFTWAREDG K:8 , DT L:11binding site for residue EDO L 101
4AC4SOFTWAREHOH D:402 , DT L:3binding site for residue EDO D 301
5AC5SOFTWAREHOH F:104 , ASP G:194 , HOH G:401binding site for residue EDO G 301
6AC6SOFTWAREDA C:8 , DA C:9 , GLN J:191binding site for residue EDO J 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XQN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XQN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XQN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XQN)

(-) Exons   (0, 0)

(no "Exon" information available for 4XQN)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee.hhh.eeee.....eeeee....eeeee.hhhhhhh....eeeee..eeee...eeeee....eeee....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4xqn A 141 ETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKK 237
                                   150       160       170       180       190       200       210       220       230       


Chain B from PDB  Type:DNA  Length:12
                                            
                 4xqn B   5 ACAGTTAAGAAT  16
                                    14  


Chain C from PDB  Type:DNA  Length:13
                                             
                 4xqn C   1 AATTCTTAACTGT  13
                                    10   


Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhh....eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4xqn D 141 ETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   150       160       170       180       190       200       210       220       230        


Chain E from PDB  Type:DNA  Length:12
                                            
                 4xqn E   5 ACAGTTAAGAAT  16
                                    14  


Chain F from PDB  Type:DNA  Length:13
                                             
                 4xqn F   1 AATTCTTAACTGT  13
                                    10   


Chain G from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhhh...eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4xqn G 141 ETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   150       160       170       180       190       200       210       220       230        


Chain H from PDB  Type:DNA  Length:12
                                            
                 4xqn H   5 ACAGTTAAGAAT  16
                                    14  


Chain I from PDB  Type:DNA  Length:12
                                            
                 4xqn I   2 ATTCTTAACTGT  13
                                    11  


Chain J from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee...eeeeee.....eeeeee...eeeee.hhhhhhh....eeeee..eeee...eeeee....eeee....eee....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4xqn J 141 ETIELKRGSNSVYVQYDDIMFFESSTKSHRLIAHLDNRQIEFYGNLKELSQLDDRFFRCHNSFVVNRHNIESIDSKERIVYFKNKEHCYASVRNVKKI 238
                                   150       160       170       180       190       200       210       220       230        


Chain K from PDB  Type:DNA  Length:11
                                           
                 4xqn K   6 CAGTTAAGAAT  16
                                    15 


Chain L from PDB  Type:DNA  Length:12
                                            
                 4xqn L   2 ATTCTTAACTGT  13
                                    11
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4XQN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XQN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XQN)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        AGRA_STAAC | Q5HEG2: 4xqj 4xqq 4xxe 4xyo 4xyq

(-) Related Entries Specified in the PDB File

4xqj 4xqq